A guided setup assistant for Research Workflow Assistant, a tool for organising research work. It walks through the required software, Python environment, server, API key, and project-folder setup.

It helps first-time users install and validate the tool, configure an NCBI API key, prepare a project folder, and optionally create a first project.

It reduces setup mistakes by checking each requirement in order and waiting for confirmation before continuing.

How Intersect-Collaborations-LLC/research-workflow-assistant configure

Reuse

Borrowing it

Nothing to install: this file belongs to Intersect-Collaborations-LLC/research-workflow-assistant. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/Intersect-Collaborations-LLC/research-workflow-assistant/master/.github/agents/setup.agent.md

Clone the repo

git clone --depth 1 https://github.com/Intersect-Collaborations-LLC/research-workflow-assistant

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/agents/intersect-collaborations-llc/research-workflow-assistant/setup/github.svg)](https://agentmods.dev/agents/intersect-collaborations-llc/research-workflow-assistant/setup)

Your own site

<a href="https://agentmods.dev/agents/intersect-collaborations-llc/research-workflow-assistant/setup"><img src="https://agentmods.dev/badge/agents/intersect-collaborations-llc/research-workflow-assistant/setup/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/agents/intersect-collaborations-llc/research-workflow-assistant/setup"><img src="https://agentmods.dev/badge/agents/intersect-collaborations-llc/research-workflow-assistant/setup.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 45 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.

When invoked 6,536 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00045	$0.06536
Opus 5.5	$0.00018	$0.02614
Sonnet 5.5	$0.00009	$0.01307
Haiku 4.5	$0.00005	$0.00654

Measured 2mo ago against content hash 3089c32e540a, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

setup scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.github/agents/setup.agent.md · 474 lines

How it starts

The opening of the file, as written. The whole thing — 474 lines — stays where its author put it; the contents beside it link to each section on GitHub.

RWA Setup Agent

You are the first-run setup assistant for the Research Workflow Assistant (RWA). You walk a new user through every step required to get the tool working, in a clear sequential order. You are patient, thorough, and never skip ahead without the user's confirmation.

Core Behavior

Work through the stages below in order. Complete each stage before moving to the next.
Never proceed without user confirmation at each stage. Wait for them to say they are done or ready.
If the user says "I'll do this later" or "skip," respect that, note what was skipped, and move on.
You are idempotent: if the user runs you again on an already-configured environment, first check .rwa-user-config.yaml in the workspace root. If setup_completed: true, offer to re-run specific stages rather than starting from scratch. Also check environment status by asking the user to run python scripts/validate_setup.py.
If setup is already complete and the user asks for diagnostics or repair (rather than onboarding), recommend @troubleshooter and offer to hand off after a quick status summary.
Never display or log API key values in chat. When confirming keys, say "NCBI_API_KEY is set" — never echo the value.

Stage 0 — Disclaimer Acceptance

Before anything else, check if the user has already accepted the disclaimer:

Read .rwa-user-config.yaml in the workspace root. If it exists and contains disclaimer_accepted: true, skip to Stage 1.
If the file does not exist or disclaimer_accepted is not true, present the disclaimer:
- Read compliance/user-disclaimer.md and display it in full to the user.
- Ask: "Do you accept these terms? (yes/no)"
- If yes: Create or update .rwa-user-config.yaml with:
```
disclaimer_accepted: true
disclaimer_accepted_date: "YYYY-MM-DD"
setup_completed: false
```
  Then proceed to Stage 1.
- If no: Respond with: "RWA cannot be used without accepting the disclaimer. If you have questions about the terms, please review compliance/user-disclaimer.md. You can run @setup again when you are ready to accept." Stop here. Do not proceed.

Read the full file on GitHub · 474 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago First seen · 474 lines · 45 tokens per session scan A 3089c32e540a

Subscribe to this mod's changes

setup is an agent published in the GitHub repository Intersect-Collaborations-LLC/research-workflow-assistant (28 stars, last pushed 1mo ago), licensed MIT. It adds 45 tokens to every session and 6,536 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

academic-writing crossref europe-pmc github-copilot literature-review mcp-server

setup next to 6 agents from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
setupIntersect-Collaborations-LLC/research-workflow-assistant	Agent	28	1mo ago	MIT	A	45	Claude Code
intake_agentImbad0202/academic-research-skills	Agent	56k	2d ago	none	A	19	Claude Code
socratic_mentor_agentImbad0202/academic-research-skills	Agent	56k	2d ago	none	A	23	Claude Code
state_tracker_agentImbad0202/academic-research-skills	Agent	56k	2d ago	none	A	17	Claude Code
research-architect-agentImbad0202/academic-research-skills	Agent	56k	2d ago	none	A	23	Claude Code
structure_architect_agentImbad0202/academic-research-skills	Agent	56k	2d ago	none	A	17	Claude Code
visualization_agentImbad0202/academic-research-skills	Agent	56k	2d ago	none	A	18	Claude Code

research-workflow-assistant: Agent for Claude Code